BMRBj - BMREntryMaster

Found 1 Document (0.732 seconds)

BMRB: 30286

5VKV

Solution NMR structure of the membrane electron transporter CcdA

Authors

Zhou, Y., Bushweller, J.H.

Assembly

Cytochrome c-type biogenesis protein CcdA

Entity

1. Cytochrome c-type biogenesis protein CcdA (polymer, Thiol state: all disulfide bound), 232 monomers, 25266.89 Da Detail

MSLSLTAAFL AGVLSFLSPC VLPLVPTYLF YLGGARGRPL FNALFFILGF GAVFFLLGLP FTLLGGLLFE HRQTLARVGG VVLVLFGLYM LGLRPRWGVS LRYEGETSRP LGAFLLGATL ALGWTPCIGP ILGAILTLTA VGGGVGFLLA YILGLAVPFF VVALFADRIK GWLRRAGRIS HYVEVLAGVV LVLVGVLLFT GTFTALNTFF LRITPEWLQR YLPSHHHHHH HH

Formula weight

25266.89 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS20:SG	1:CYS127:SG

Source organism

Thermus thermophilus HB8

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.9 %, Completeness: 41.5 %, Completeness (bb): 69.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	41.5 % (1140 of 2748)	25.5 % (354 of 1388)	52.7 % (596 of 1132)	83.3 % (190 of 228)
Backbone	69.5 % (951 of 1368)	47.7 % (230 of 482)	80.2 % (534 of 666)	85.0 % (187 of 220)
Sidechain	20.0 % (317 of 1582)	13.8 % (125 of 906)	28.3 % (189 of 668)	37.5 % (3 of 8)
Aromatic	7.1 % (25 of 354)	5.6 % (10 of 177)	6.9 % (12 of 173)	75.0 % (3 of 4)
Methyl	22.0 % (83 of 378)	19.6 % (37 of 189)	24.3 % (46 of 189)

1. entity 1

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 343 K, pH 5.5, Details 0.37 mM [U-13C; U-15N; U-2H] CcdA, 25 mM sodium acetate, 25 mM potassium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
1	CcdA	[U-13C; U-15N; U-2H]	0.37 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium acetate	natural abundance	25 mM
4	sodium azide	natural abundance	0.05 %
5	sodium chloride	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 343 K, pH 5.5, Details 0.7 mM [U-15N; U-2H] CcdA, 25 mM sodium acetate, 25 mM potassium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
6	CcdA	[U-15N; U-2H]	0.7 mM
7	potassium phosphate	natural abundance	25 mM
8	sodium acetate	natural abundance	25 mM
9	sodium azide	natural abundance	0.05 %
10	sodium chloride	natural abundance	50 mM

Sample #3

#	Name	Isotope labeling	Concentration
11	CcdA	[U-15N; U-2H]	0.7 mM
12	potassium phosphate	natural abundance	25 mM
13	sodium acetate	natural abundance	25 mM
14	sodium azide	natural abundance	0.05 %
15	sodium chloride	natural abundance	50 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 343 K, pH 5.5, Details 0.2 mM [U-15N] CcdA single Cys mutants labeled with MTSL, 25 mM sodium acetate, 25 mM potassium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
16	CcdA single Cys mutants labeled with MTSL	[U-15N]	0.2 mM
17	potassium phosphate	natural abundance	25 mM
18	sodium acetate	natural abundance	25 mM
19	sodium azide	natural abundance	0.05 %
20	sodium chloride	natural abundance	50 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 5VKV, Strand ID: A Detail

Release date

2017-04-26

Citation

Solution structure and elevator mechanism of the membrane electron transporter CcdA
Zhou, Y., Bushweller, J.H.
Nat. Struct. Mol. Biol. (2018), 25, 163-169, PubMed 29379172 , DOI 10.1038/s41594-018-0022-z , Abstract

Related entities 1. Cytochrome c-type biogenesis protein CcdA, : 1 : 45 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 343 K, pH 5.5, Details 0.37 mM [U-13C; U-15N; U-2H] CcdA, 25 mM sodium acetate, 25 mM potassium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
1	CcdA	[U-13C; U-15N; U-2H]	0.37 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium acetate	natural abundance	25 mM
4	sodium azide	natural abundance	0.05 %
5	sodium chloride	natural abundance	50 mM

2 3D HNCA

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-13C; U-15N; U-2H]	0.37 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium acetate	natural abundance	25 mM
4	sodium azide	natural abundance	0.05 %
5	sodium chloride	natural abundance	50 mM

3 3D HN(CO)CA

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-13C; U-15N; U-2H]	0.37 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium acetate	natural abundance	25 mM
4	sodium azide	natural abundance	0.05 %
5	sodium chloride	natural abundance	50 mM

4 3D HNCO

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-13C; U-15N; U-2H]	0.37 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium acetate	natural abundance	25 mM
4	sodium azide	natural abundance	0.05 %
5	sodium chloride	natural abundance	50 mM

5 3D HN(CA)CO

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-13C; U-15N; U-2H]	0.37 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium acetate	natural abundance	25 mM
4	sodium azide	natural abundance	0.05 %
5	sodium chloride	natural abundance	50 mM

6 3D HNCACB

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-13C; U-15N; U-2H]	0.37 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium acetate	natural abundance	25 mM
4	sodium azide	natural abundance	0.05 %
5	sodium chloride	natural abundance	50 mM

7 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-13C; U-15N; U-2H]	0.37 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium acetate	natural abundance	25 mM
4	sodium azide	natural abundance	0.05 %
5	sodium chloride	natural abundance	50 mM

8 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 343 K, pH 5.5, Details 0.7 mM [U-15N; U-2H] CcdA, 25 mM sodium acetate, 25 mM potassium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
6	CcdA	[U-15N; U-2H]	0.7 mM
7	potassium phosphate	natural abundance	25 mM
8	sodium acetate	natural abundance	25 mM
9	sodium azide	natural abundance	0.05 %
10	sodium chloride	natural abundance	50 mM

9 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
11	CcdA	[U-15N; U-2H]	0.7 mM
12	potassium phosphate	natural abundance	25 mM
13	sodium acetate	natural abundance	25 mM
14	sodium azide	natural abundance	0.05 %
15	sodium chloride	natural abundance	50 mM

10 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 343 K, pH 5.5, Details 0.2 mM [U-15N] CcdA single Cys mutants labeled with MTSL, 25 mM sodium acetate, 25 mM potassium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
16	CcdA single Cys mutants labeled with MTSL	[U-15N]	0.2 mM
17	potassium phosphate	natural abundance	25 mM
18	sodium acetate	natural abundance	25 mM
19	sodium azide	natural abundance	0.05 %
20	sodium chloride	natural abundance	50 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_30286_5vkv.nef
Input source #2: Coordindates	5vkv.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:20:CYS:SG	A:127:CYS:SG	unknown, CA 55.9177 ppm	unknown, CA 58.9243 ppm	2.026

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MSLSLTAAFLAGVLSFLSPCVLPLVPTYLFYLGGARGRPLFNALFFILGFGAVFFLLGLPFTLLGGLLFEHRQTLARVGGVVLVLFGLYMLGLRPRWGVS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSLSLTAAFLAGVLSFLSPCVLPLVPTYLFYLGGARGRPLFNALFFILGFGAVFFLLGLPFTLLGGLLFEHRQTLARVGGVVLVLFGLYMLGLRPRWGVS

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
LRYEGETSRPLGAFLLGATLALGWTPCIGPILGAILTLTAVGGGVGFLLAYILGLAVPFFVVALFADRIKGWLRRAGRISHYVEVLAGVVLVLVGVLLFT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LRYEGETSRPLGAFLLGATLALGWTPCIGPILGAILTLTAVGGGVGFLLAYILGLAVPFFVVALFADRIKGWLRRAGRISHYVEVLAGVVLVLVGVLLFT

-------210-------220-------230--
GTFTALNTFFLRITPEWLQRYLPSHHHHHHHH
||||||||||||||||||||||||||||||||
GTFTALNTFFLRITPEWLQRYLPSHHHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	232	0	0	100.0

Content subtype: combined_30286_5vkv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	880		88.8 (chain: A, length: 232)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	151 (1)	noe	57.3 (chain: A, length: 232)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	370 (370)	.	87.1 (chain: A, length: 232)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	100 (100)	.	43.1 (chain: A, length: 232)
2	RDC restraints	CNS/XPLOR_dipolar_coupling_7	OK	107 (107)	.	46.1 (chain: A, length: 232)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 232, Sequence coverage: 88.8%
- Total number of assignments
  - ¹³C chemical shifts: 509
  - ¹H chemical shifts: 186
  - ¹⁵N chemical shifts: 185
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	1132	509	45.0
¹H chemical shifts	1388	186	13.4
¹⁵N chemical shifts	242	185	76.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	464	396	85.3
¹H chemical shifts	482	183	38.0
¹⁵N chemical shifts	220	182	82.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	668	113	16.9
¹H chemical shifts	906	3	0.3
¹⁵N chemical shifts	22	3	13.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	191	17	8.9
¹H chemical shifts	191	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	173	0	0.0
¹H chemical shifts	177	3	1.7
¹⁵N chemical shifts	4	3	75.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 232, Sequence coverage: 57.3%
- Total number of restraints: 151
- Weight of restraints: 1.0 (151)
- Potential type of restraints: square-well-parabolic (151)
- Range of distance target values: 2.4, 3.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 232, Sequence coverage: 87.1%
- Total number of restraints: 370
- Total number of restraints per polymer type: 370
- Weight of restraints: 1.0 (370)
- Potential type of restraints: square-well-parabolic (370)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 232, Sequence coverage: 43.1%
- Total number of restraints: 100
- Potential type of restraints: undefined (100)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
- Saveframe: CNS/XPLOR_dipolar_coupling_7
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 232, Sequence coverage: 46.1%
  - Total number of restraints: 107
  - Potential type of restraints: undefined (107)
  - Range of observed RDC values: 100.0, -100.0 (Hz)
  - RDC restraints per residue

Keywords DsbD, Membrane transporter, Oxidoreductase

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Found 1 Document (0.732 seconds)

BMRB: 30286

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. Cytochrome c-type biogenesis protein CcdA, : 1 : 45 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 6 contents Detail